X-133991764-A-T

Variant names:

• chrX-133991764-A-T
• rs7883190

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.483 in 110,019 control chromosomes in the GnomAD database, including 10,053 homozygotes. There are 15,362 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (10053 hom., 15362 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.483 AC: 53129 AN: 109966 Hom.: 10051 Cov.: 22

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.480

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.483 AC: 53133 AN: 110019 Hom.: 10053 Cov.: 22 AF XY: 0.475 AC XY: 15362 AN XY: 32315

African (AFR) AF: 0.308 AC: 9323 AN: 30285

American (AMR) AF: 0.363 AC: 3772 AN: 10382

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 1769 AN: 2619

East Asian (EAS) AF: 0.205 AC: 707 AN: 3450

South Asian (SAS) AF: 0.562 AC: 1422 AN: 2531

European-Finnish (FIN) AF: 0.538 AC: 3070 AN: 5711

Middle Eastern (MID) AF: 0.656 AC: 141 AN: 215

European-Non Finnish (NFE) AF: 0.602 AC: 31683 AN: 52651

Other (OTH) AF: 0.479 AC: 721 AN: 1504

Alfa AF: 0.560 Hom.: 4238

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7883190; hg19: chrX-133125791;